What are RNA foci?

RNA foci are abnormal structures that form in cells due to particular RNA molecules adopting abnormal conformations or accumulating in high concentrations found in some neurodegenerative diseases. These aggregates disrupt normal cellular functions by sequestering RNA-binding proteins, leading to dysregulation of RNA metabolism. These structures are often associated with various neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), myotonic dystrophy (DM), and fragile X-associated tremor/ataxia syndrome (FXTAS).

Investigating RNA foci holds promise for understanding disease mechanisms and developing novel treatments for associated neurodegenerative disorders.

RNA-RNA binding protein complexes or aggregates form insoluble nuclear foci that cause cellular defects. RNA foci are a result of expanding RNA repeats. The expanded RNA repeats are retained in the nucleus, adopt unusual secondary structures, sequester various RNA-binding proteins, and can become toxic to the cell. The abnormal expansion of nucleotide repeats can lead to numerous effects on genes, such as the inhibition of transcription and the loss of function of proteins, leading to disease.

The expansion of repeated nucleotide sequences within specific genes typically forms RNA foci. In normal circumstances, these repeated sequences are present in limited copie numbers. However, the number of repeats in certain diseases increases beyond a critical threshold. The expanded RNA molecules tend to fold into secondary structures, such as hairpins or stem-loops, promoting the formation of RNA foci.

The RNA foci are aggregates of multiple RNA molecules closely associated with proteins and other cellular components. 

Special imaging techniques enable the observation of these aggregates. These include fluorescence in situ hybridization (FISH) or immunofluorescence, allowing researchers to visualize and study their properties.

The formation of RNA foci has been implicated in the pathogenesis of several neurodegenerative diseases. Simple microsatellite expansions, usually consisting of 3 to 6 nucleotides, cause these diseases. The repeats can occur in non-coding regions. The result is a dominantly inherited disease characteristic of a toxic RNA gain-of-function disease. Numerous central nervous tissues appear to contain RNA foci. Repeat RNA foci can differ in size, shape, cellular abundance, and protein composition, but their formation harms cellular functions. In humans, the expansion of short tandem repeats of tri-, tetra-, and pentanucleotides in single genes cause these hereditary neurological diseases. The expanded repeat tract can also be located in protein-coding sequences and affect the final gene product of the mutant gene.

For example, in ALS, RNA foci containing the mutant form of the superoxide dismutase 1 (SOD1) gene have been observed in affected motor neurons. These foci sequester RNA-binding proteins, such as TDP-43, causing dysregulation of RNA metabolism and cellular dysfunction.

Similarly, in DM, expanded repeats in the DMPK gene form RNA foci that sequester muscleblind-like (MBNL) proteins. This sequestration leads to the misregulation of alternative splicing and contributes to the characteristic symptoms of the disease, including muscle weakness and myotonia.

In FXTAS, a neurodegenerative disorder associated with the expansion of CGG repeats in the FMR1 gene, RNA foci containing the expanded CGG repeats accumulate in various tissues, including the brain. These foci sequester specific proteins, such as Sam68, and disrupt cellular functions, leading to the neurodegenerative symptoms observed in affected individuals.

Understanding the mechanisms underlying RNA foci formation and their role in disease pathology is an active area of research. Researchers are investigating approaches to prevent or dissolve these aggregates, aiming to develop potential therapeutic strategies for neurodegenerative diseases associated with RNA foci.


Walsh MJ, Cooper-Knock J, Dodd JE, et al. Invited Review: Decoding the pathophysiological mechanisms that underlie RNA dysregulation in neurodegenerative disorders: a review of the current state of the art. Neuropathology and Applied Neurobiology. 2015;41(2):109-134. [ Pubmed]

Rohilla KJ, Gagnon KT. RNA biology of disease-associated microsatellite repeat expansions. Acta Neuropathologica Communications. 2017;5:63.[ 

Wojciechowska M, Krzyzosiak WJ. Cellular toxicity of expanded RNA repeats: focus on RNA foci. Human Molecular Genetics. 2011;20(19):3811-3821. [ PMC ]


Fluorescence in situ hybridization (FISH) allows for the detection and localization of specific sequences of nucleic acids inside cells or tissue. FISH antisense probes hybridizing to specific RNA transcript sequences allow distinguishing the presence of particular transcripts the contain simple repeat expansions. FISH enables the detection of a variable number of RNA foci scattered throughout the nucleus in cells expressing mutant RNA. In recent years ribonucleoprotein foci of repeated CUG, CCUG, CGG, CAG, AUUCU and UGGAA motifs present in different tissues have been characterized in more detail.  

Myotonic dystrophy

In myotonic dystrophy type 1 (DM1) which is a multisystemic disease, the cause is an expanded CTG repeat in the 3-untranslated region (UTR) of the dystrophia myotonica protein kinase (DMPK) gene. The expanded CUG repeat RNA (CUGn RNA) is retained in the nucleus where it forms RNA foci. DM1 leads to defects in regulated alternative splicing events during development. In DM1 the RNA foci sequester the muscleblind like splicing regulator ( MBNL) family of splicing factors and induce upregulation of CELF1 activity through PKC-mediated phosphorylation and altered microRNA regulation.

DM1 and DM2 repeating RNAs are not translated into protein. DM1 is caused by an expansion of a CUG repeat in the 3′ untranslated region (UTR) of the dystrophia myotonica protein kinase (DMPK) mRNA. DM2 is caused by an expansion of a CCUG repeat in intron 1 of the zinc finger 9 protein (ZNF9) pre-mRNA. The model for how these RNAs contribute to DM1 and DM2 describes an RNA gain-of-function that occurs upon expansion. In the model, long, toxic repeats fold into hairpins and bind the RNA splicing regulator muscleblind-like protein 1 (MBNL1). Sequestering of MBNL1 caused by the repeating RNAs causes splicing defects in a subset of pre-mRNAs, including the insulin receptor and the muscle main chloride ion channel.


Figure 1: Structural Models of the Triplet Repeat in Myotonic Dystrophy. Synthetic RNA was used for the folding and assembly of the RNA duplex. A sitting drop vapor diffusion method was used for crystallization, and a beam line at the Advanced Photo source at Argonne National Laboratory was used for collecting the diffraction data sets of crystals.

(Ref.: Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 x 1 nucleotide UU internal loop conformations. Kumar A, Park H, Fang P, Parkesh R, Guo M, Nettles KW, Disney MD; Biochemistry (2011) 50 p.9928-9935. PDB ID 3SZX).


The MBNL 1 gene encodes a member of the muscleblind protein family which was initially described in Drosophila melanogaster. The encoded protein is a C3H-type zinc finger protein that modulates alternative splicing of pre-mRNAs. Muscleblind proteins bind specifically to expanded dsCUG RNA but not to normal size CUG repeats and may thereby play a role in the pathophysiology of myotonic dystrophy.


MBNL1 gene: https://www.ncbi.nlm.nih.gov/gene/4154 

Muscleblind-like protein 1: 


Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. It is thought that this gene may play a role in myotonic dystrophy type 1 (DM1) via interactions with the dystrophia myotonica-protein kinase (DMPK) gene. Alternative splicing results in multiple transcript variants encoding different isoforms. The members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains.


CELF1 gene:  

CAG expansion disorders

In the CAG expansion disorders Huntington’s disease (HD), X-linked spinal and bulbar muscular atrophy (SBMA), X-linked spinal and bulbar muscular atrophy (DRPLA), and spinocerebellar ataxia type disorders (SCA1, SCA2, SAC3/MJD, SCA7 and SCA17) the molecular pathogenesis appears to be primarily mediated by a deleterious gain of function of the polyglutamine tract encoded by the expanded trinucleotide sequence.


Triplet Repeat Diseases: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913379/

Huntington disease: